Rapid identification and interpretation of gene–environment associations using the new R.SamBada landscape genomics pipeline

sam βada is a genome–environment association software, designed to search for signatures of local adaptation. However, pre‐ and postprocessing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an r ‐package providing a pipeline for landscape genomic analysis based on sam βada , spanning from the retrieval of environmental conditions at sampling locations to gene annotation using the Ensembl genome browser. As a result, R.SamBada standardizes the landscape genomics pipeline and eases the search for candidate genes of local adaptation, enhancing reproducibility of landscape genomic studies. The efficiency and power of the pipeline is illustrated using two examples: sheep populations from Morocco with no evident population structure and Lidia cattle from Spain displaying population substructuring. In both cases, R.SamBada enabled rapid identification and interpretation of candidate genes, which are further discussed in the light of local adaptation. The package is available in the r CRAN package repository and on GitHub (github.com/SolangeD/R.SamBada).     

Infrastructure and the environment in the Anthropocene

For centuries, man‐made infrastructure has been viewed as separate from natural systems. Yet in the past few centuries, as the scale and scope of human activities have dramatically increased, there is accumulating evidence that natural systems are becoming increasingly, and in some cases entirely, managed by humans. The dichotomy between infrastructure and the environment is narrowing, and natural systems are increasingly becoming human design spaces. This is already apparent with the management of hydrologic systems for urban water supply, wildlife, agriculture, forests, and even the atmosphere, and we can expect management of the environment to become more so as human activities grow. Yet our infrastructure largely remains obdurate. They are designed to last for long times even as changes in the environment and technology accelerate. As such, our current infrastructure paradigms fail at the level of the complex, integrated systems and behaviors that characterize the Anthropogenic Earth. Infrastructure in the future will need to be designed for adaptive capacity and the complexities associated with techno‐environmental systems.     

工业环境下酶蛋白的催化行为与适应性改造研究进展

酶在工业上有着广泛应用和巨大潜力,但工业生产中高温、强酸/碱、高盐、有机溶剂和高底物浓度等条件仍然制约着酶的大规模应用。为使酶能更好地在工业环境下发挥催化作用,目前的主要策略是对酶进行适应性改造(如理性或半理性设计、定向进化、固定化等)。文中简要阐述了酶在工业环境下的催化行为以及近年对其适应性改造的研究进展,以期为酶的适应性改造提供参考。     

公众对园林绿地功能的认知及其对环境教育的启示——以广州市为例

以网络问卷和现场问卷、访谈的形式,分析公众对广州市园林绿地功能的认知情况,以期为环境教育场地的建设提供参考。结果显示,公众对于物种多样性和景观多样性的各项具体描述的认知情况都趋于一致,绝大多数公众认为绿地植被能发挥重要的生态功能,且公众的学历越高,其认知园林植物的欲望越强烈。在休息时,大多数公众会选择植物比较茂密的半开敞空间;在园林设计中通过增强科普信息获取的便利性和趣味性,能更好地发挥绿地的环境教育功能。     

Landscape genetic structure of Scirpus mariqueter reveals a putatively adaptive differentiation under strong gene flow in estuaries

Estuarine organisms grow in highly heterogeneous habitats, and their genetic differentiation is driven by selective and neutral processes as well as population colonization history. However, the relative importance of the processes that underlie genetic structure is still puzzling. Scirpus mariqueter is a perennial grass almost limited in the Changjiang River estuary and its adjacent Qiantang River estuary. Here, using amplified fragment length polymorphism (AFLP), a moderate‐high level of genetic differentiation among populations (range F_ST: 0.0310–0.3325) was showed despite large ongoing dispersal. FLOCK assigned all individuals to 13 clusters and revealed a complex genetic structure. Some genetic clusters were limited in peripheries compared with very mixing constitution in center populations, suggesting local adaptation was more likely to occur in peripheral populations. 21 candidate outliers under positive selection were detected, and further, the differentiation patterns correlated with geographic distance, salinity difference, and colonization history were analyzed with or without the outliers. Combined results of AMOVA and IBD based on different dataset, it was found that the effects of geographic distance and population colonization history on isolation seemed to be promoted by divergent selection. However, none‐liner IBE pattern indicates the effects of salinity were overwhelmed by spatial distance or other ecological processes in certain areas and also suggests that salinity was not the only selective factor driving population differentiation. These results together indicate that geographic distance, salinity difference, and colonization history co‐contributed in shaping the genetic structure of S. mariqueter and that their relative importance was correlated with spatial scale and environment gradient.     

A general kinetic model for biological nutrient removal activated sludge systems: model development

In this article, a kinetic model is developed and presented for biological nutrient removal (BNR) activated sludge (BNRAS) systems in general, but for external nitrification (EN) BNRAS (ENBNRAS) systems in particular. The model is based on the UCTPHO model, but includes some significant modifications, such as anoxic P uptake and associated denitrification by phosphorus accumulating organisms (PAOs). Some key features of the model are described and discussed before the model is presented. Model evaluation will be addressed in another article (Hu et al., 2007).     

特定频谱波对水电导率影响的研究

目的:为了研究特定频谱波引起的水中离子浓度的变化以及电导率与频谱波间相互作用的规律,用特定频谱波对理化特性略有不同的纯净水、自来水、海水进行影响,研究其电导率的变化。方法:采用一元线性回归分析的方法对数据散点进行拟和,用方差分析来评价其拟合效果,以期发现其中的规律。结果:经过频谱波的影响各种水的电导率都有明显的提高,并且随着处理次数的增加,纯净水的电导率呈阶越式方式增加;自来水呈对数形式增加;而海水则表现为变化幅度微小。结论:造成这个现象的原因可能是由于水分子吸收了频谱波的能量,分子的平均动能增大造成的。这一过程使化学平衡(H2O)n≒xH2O (H2O)n-x和H2O≒ H OH-均向分解的方向运动,水中带电离子的浓度提高,因此电导率发生变化。而电导率提高方式的差异,则是水样在理化特性上的差异导致的。     

Heavy metal-induced selection and proliferation of antibiotic resistance: A review

Antibiotic resistance is recognized as a global threat to public health. The selection and evolution of antibiotic resistance in clinical pathogens were believed to be majorly driven by the imprudent use of antibiotics. However, concerns regarding the same, through selection pressure by a multitude of other antimicrobial agents, such as heavy metals, are also growing. Heavy metal contamination co-selects antibiotic and metal resistance through numerous mechanisms, such as co-resistance and cross-resistance. Here, we have reviewed the role of heavy metals as antimicrobial resistance driving agents and the underlying concept and mechanisms of co-selection, while also highlighting the scarcity of studies explicitly inspecting the process of co-selection in clinical settings. Prospective strategies to manage heavy metal-induced antibiotic resistance have also been deliberated, underlining the need to find specific inhibitors so that alternate medicinal combinations can be added to the existing therapeutic armamentarium.